Precision ID NGS System for human identification

The Applied Biosystems™ Precision ID NGS System for human identification can help you solve tough cases by getting more information from your challenging samples. Adopting NGS (next-generation sequencing) for forensic DNA analysis in your laboratory is now simpler than ever, when you combine the Ion Chef™ System and Ion S5™ or Ion S5™ XL Systems with forensically relevant Precision ID panels that utilize Ion AmpliSeq™ technology.

With as little as 1 ng of DNA input, you can quickly and easily analyze your challenging casework samples with as few as 5 pipetting steps and 45 minutes of hands-on time.

The Applied Biosystems™ Precision ID GlobalFiler™ NGS STR Panel includes the same 21 autosomal STRs, along with a Y indel and amelogenin sex markers found in the GlobalFiler DNA amplification kit. Instead of using SE33, this panel includes 9 additional multiallelic STR markers (for a total of 33 targets) to aid in mixture interpretation for complex casework samples. Using minimal input of 1 ng of DNA, this targeted forensic marker panel enables sample extraction to genotypes in less than two days using the HID STR Genotyper plug-in.

The Precision ID GlobalFiler NGS STR Panel provides both allele number and base sequence for each repeat structure, offering enhanced mixture resolution and increased Probability of Identity (PI) estimates. The Precision ID GlobalFiler NGS STR Panel is currently available for use with manual library preparation, template preparation on the Ion Chef™ System or Ion OneTouch™ 2 System, and sequencing on the Ion PGM™ System.

The Applied Biosystems™ Precision ID mtDNA Whole Genome Panel is an innovative approach to mitochondrial DNA sequencing specifically developed for forensic applications. This mtDNA tiling approach includes two primer pools of 81 small amplicons in each pool, with an average size of 163 bp, to assist with obtaining optimal mitochondrial genome coverage data from highly compromised, degraded samples such as hair shafts, teeth, and bones.

Whole genome coverage of 4 samples of ancient tooth and bone samples was generated using 1 ng of input DNA, automated library preparation using the Ion Chef System, and sequencing on the Ion S5 System. The small amplicon design and inclusion of degenerate primers in the Precision ID mtDNA Whole Genome Panel increases success with degraded and low-starting-template DNA.

The Applied Biosystems™ Precision ID mtDNA Control Region Panel is based on the same mtDNA tiling approach used in the Precision ID mtDNA Whole Genome Panel. This targeted control region panel contains two smaller sets of primer pools with 7 amplicons each that span the 1.2 kb control region, which encompasses HV-I, II, and III, with the same optimal coverage for degraded forensic samples.

Precision ID Ancestry Panel

Ion AmpliSeq technology enables simple, fast target selection of hundreds of SNPs using multiplex PCR. Thousands of primer pairs can be used in a single tube for target amplification followed by next-generation sequencing (NGS) on the Applied Biosystems™ Precision ID NGS System. Utilizing this technology for human identification (HID) applications, the Precision ID Ancestry Panel can provide you with biogeographic ancestry information and guide your investigation process. Alternatively, it may help identify or stratify the subjects for your research projects.

This ready-to-use panel includes 165 autosomal markers that provide biogeographic ancestry information. 55 of these markers were selected based on a publication by Dr. Kenneth Kidd [1], and 123 markers were selected based on a publication by Dr. Michael Seldin [2]. Ion AmpliSeq technology makes it possible to multiplex 165 PCR reactions in one tube with only 1 ng of input DNA. With small amplicon sizes, the panel is also optimized for degraded DNA samples.

24 samples of known genotype were analyzed after one run on the Ion PGM System using the Ion 318™ Chip v2. The sequencing reads were analyzed using Torrent Suite™ Software, Variant Caller 4.0, and the HID SNP Genotyper™ plug-in. Results from the study demonstrated a concordance rate of 99.77% for the 55 SNPs from Dr. Kenneth Kidd at an average read depth of ~1,250x per SNP.

Analyze highly degraded or trace DNA

Precision ID Identity Panel

Single-nucleotide polymorphisms (SNPs) provide a variety of new, important information for human identification purposes, in addition to short tandem repeats (STRs). Due to the shorter amplicons required for sequencing, SNPs enable high recovery of information from degraded samples—such as from mass disaster victims.

The Applied Biosystems™ Precision ID Identity Panel includes 124 autosomal markers, and provides discrimination of individuals similar to STR genotype match probabilities used by forensic analysts (between 1 x 10-31 and 6 x 10-35). The high discrimination power is achieved by using 34 upper Y-clade SNPs and 90 autosomal SNPs that have high heterozygosity and low Fixation Index (Fst), described in publications by Kenneth Kidd of Yale University [3] and the SNPforID Consortium [4,5].

32 samples were analyzed after one run on the Ion PGM System using the Ion 318 Chip v2. The sequencing reads were analyzed using Torrent Suite Software, Variant Caller 4.0, and the HID SNP Genotyper plug-in. A set of 46 SNPs (all 43 unlinked SNPs from Dr. Kenneth Kidd and 3 additional SNPforID SNPs) were evaluated in a concordance study with results demonstrating a concordance rate of 99.99% at an average read depth of ~750x per autosomal SNP and ~350x per Y SNP.

Save time at the bench, help improve your laboratory’s productivity, and standardize your results. The Ion Chef System for human identification performs the repetitive lab work without the need for complex robotics and confusing scripts. Paired with Ion Torrent™ next-generation sequencing platforms, the Ion Chef System automates Precision ID library preparation, template generation, and chip loading with push-button simplicity—enabling DNA to data in as little as 45 minutes of hands-on time.

Ion Chef System templating and chip loading workflow

1Library Preparation

Load reagents & consumables

Load library samples

Set run parameters

2Automated template preparation and chip loading

Library amplification

ISP recovery & enrichment

Chip loading

3Sequencing

Run sequence on either:

Ion S5 System

Ion PGM System

Suitable for scientists and researchers in forensic human identification, the Ion Chef System offers automated workflows that help enable gains in laboratory efficiency. Unleash the power of the Precision ID NGS System with Ion Chef System automation, paired with Ion AmpliSeq technology which is used in the Precision ID Panels for human identification.

Automates library generation, equalization, and pooling for 1- and 2-pool designs for up to 8 samples in a single instrument run

Operates with a very low inter-run cross-contamination rate of <0.01%

Helps reduce sources of variability for forensic scientists of any experience level

Want to sequence SNP panels on Monday, mtDNA panels on Wednesday, and STR panels on Thursday? The Ion S5 Systems, an integral part of the Precision ID NGS System, or the Ion PGM™ System let you leverage a single benchtop instrument that scales to your application and throughput needs. The Ion S5 and Ion S5 XL Systems provide the simplest DNA-to-data workflow for targeted sequencing with industry-leading speed and affordability, and the flexibility to multiplex and optimize the number of samples and panels on a single chip.

Simplicity: ready, set, sequence

Less than 15 minutes of sequencer hands-on time

Less than 45 minutes of hands-on time for a DNA-to-data targeted sequencing workflow

Simple data analysis and storage

Service and support

More than 3,700 global sales, service, and technical support specialists are available to assist you in person, by phone, or online—including our Human Identification Professional Services (HPS) team that can help you successfully navigate the validation process required to bring new technologies into your lab.

Raw data, base calling, variant calling, and genotyping are processed on the Ion S5 Sequencer; or, in the case of the Ion S5 XL System, transferred to a dedicated Ion S5 Torrent Server for faster analysis. Torrent Suite Software is used to plan runs and for plug-in analysis.

By expanding the functionality of the current on-board software, plug-ins offer a powerful means to manage a full range of HID applications. Torrent Suite Software allows you to customize your analysis at the end of each run through the use of different plug-ins available in the Ion Community.

Torrent Variant Caller (TVC) is a genetic variant caller and is specially optimized to exploit the underlying flow signal information in the statistical model to evaluate variants. TVC can be used to analyze mtDNA data at both the whole genome and control region panels.

HID SNP Genotyper is a plug-in designed to be an integrated tool, providing streamlined analysis and reporting for the Precision ID Identity Panel and Ancestry Panel. It uses the Torrent Variant Caller to identify the genotypes at specific hotspot locations, performs bio-geo ancestry Y lineage prediction, and computes Random Match Probability (RMP).

The HID STR Genotyper plug-in analyzes sequencing data from short tandem repeat regions and generates allele calls along with their sequence content. Interactive allele coverage charts and quality metrics for each locus simplify the complexity of analyzing STRs using next-generation sequencing. The allele calls can then be exported and utilized for further downstream applications like mixture analysis or database searches.

Customer videos

Mitochondrial DNA analysis in human identification

Imagine that you have a small, aged bone fragment or charred remains after a fire, a tooth that has been buried and exposed to the environment for years to decades, or possibly a single hair shaft. How would you even begin to make an identification to reconnect these remains with family members? Walther Parson, PhD from the Institute of Legal Medicine, Innsbruck Medical University discusses a number of cases his lab has worked on, using mtDNA analysis to make critical identifications.

Next-generation sequencing and the ability to multiplex many markers for a single sample has gained acceptance within the forensic community. There are a number of SNP classifications that are currently being investigated, including identity SNPs, phenotypic SNPs, and biogeographic ancestry SNPs. Executive Director Soizic Le-Gunier discusses how Institute Genetics Nantes Atlantique (IGNA) uses the various technology options, and how SNP genotyping will have an impact in the future.